Debian Wheezy Logging Issues – No More Logging After Upgrade

I'm not sure where the & ~ comes from, but at least the following should perform what you want:

# Iptables
:msg,contains,"IPT IN/DP: " -/var/log/iptables.log
:msg,contains,"IPT6 IN/DP: " -/var/log/iptables.log
:msg,contains,"IPT IN/DP: " ~
:msg,contains,"IPT6 IN/DP: " ~

Maybe not most elegant, but a similar config seems to work for me.

Now I stumbled upon the solution by myself. The problem is caused by an update of mod_fcgid which changed the directives used in the vhost configs. The changes could be seen here (this is what I stumbled upon).

The directive

FCGIWrapper /var/www/example.com/php-fcgi/php-fcgi-starter .php

has to be changed to

FcgidWrapper /var/www/example.com/php-fcgi/php-fcgi-starter .php

The documentation says

"All directives have been renamed in order to use a common prefix "Fcgid". Underscores in directive names have been eliminated in favor of CamelCase. The old directive names will still work but are deprecated. To fix your configuration you can use the sed script build/fixconf.sed."

but it seems like the old directive names didn't work anymore for now. The changes have done the trick for me, maybe this will help someone else.